Dear group,

I am trying to perform Charm analysis on a dataset consisted of 24 two
channel NimbleGen Promoter Medip Arrays. Our data represent same patients'
methylation levels before and after treatment so it is a paired design.

My problem is, getting an error which I don't understand and don't know how
to solve.

 >setwd("~/Desktop/mydata")
>dataDir<-getwd()
> pd<-read.delim(file.path(dataDir,"phenoData.txt"))
> rawData<-readCharm(files=pd$filename, path=dataDir, sampleKey=pd)
> ctrlIdx<-getControlIndex(rawData,subject=Hsapiens)
>
pData(rawData)$pair=c(1,2,7,4,2,6,3,3,4,5,5,1,7,10,9,9,10,6,8,11,11,8,12,12)
> p<- methp(rawData, controlIndex=ctrlIdx, plotDensity="density.pdf",
plotDensityGroups=grp)
Spatial normalization
Background removal
Error in density.default(x, kernel = "epanechnikov", n = n.pts, na.rm =
TRUE) : need at least 2 points to select a bandwidth automatically

I am running the analysis on a "x86_64-apple-darwin10.8.0" and R version
3.0.0

Is it related to big data size? How can I solve this?

Thank you in advance,

Zeynep Ozkeserli
Ankara University Biotechnology Institute

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